The course is open for PhD students, postdocs, researchers and other employees in need of Linux command line skills within all universities.

Important dates

Application opens: 2019-09-12

Application closes: 2019-11-08, 12 am

Confirmation to accepted students: one week after application closes

Responsible teachers: Mihaela Martis-Thiele & Jeanette Tångrot

If you do not receive information according to the above dates please contact: mihaela.martis@nbis.se

Course fee

A course fee* of 1300 SEK will be invoiced to accepted participants in the classroom in Stockholm and Umeå. This includes lunches, coffee and snacks. There are no costs for the remaining participants.

*Please note that NBIS cannot invoice individuals

Course content

NBIS (the Swedish node of ELIXIR) and ELIXIR Slovenia are offering an “Introduction to Linux” course targeted at life scientists who want to extend their skills and knowledge. The course is delivered via classroom training and via an e-learning platform, thus offering the participants the possibility of attending the course either by traveling to Stockholm or to Umeå in Sweden, to Ljubljana in Slovenia, or by connecting remotely via the ELIXIR Slovenia e-learning platform. The number of remote students is limited to 30. The course will be broad-casted from Sweden.

Topics covered will include:

Introduction to the Unix/Linux operating system

Filesystem structure & navigating the filesystem

Searching the filesystem

Viewing and editing files

Text processing commands

File/directory ownership & permissions

I/O redirections

Compression of files/directories

Fundamental shell scripting

Exercises – applying learned shell commands

Course certificates will be handed out only if sufficient points are earned during small accompanying exams. Participation to the exams is not mandatory if a certificate is not needed.

Entry requirements

The course is addressed to life scientists with no or very little experience in using Linux commands, but who are enthusiastic about learning how to use them for simplifying their work and improving their efficiency. Participants should expect an INTENSIVE COURSE which includes many hands-on exercises.

All participants are expected to use their own computers. In addition, remote participants are expected to have an (integrated) web-cam and a headset, so that we can give you quick feedback and efficient help.

Registration

To register please use the following link: https://linux2019.eventbrite.co.uk

Due to limited space the course can accommodate maximum of 15 participants in the individual classrooms in Stockholm and Umea, 20 in Ljubljana, and 30 remote participants.

Every 1st week of the month (mainly on Tuesdays, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate.

The ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji, CellProfiler, KNIME, QuPath, Ilastik), but also commercial systems, if needed (Imaris).

How to participate?

Step1:

Prepare a short presentation (5-7 min) – use the following template for your presentation:

Tuesday December 10 at 15:00

Gail A. Robertson,

Gail Robertson is a molecular biologist and biophysicist interested mechanisms controlling electrical excitability in the heart and brain. She received her PhD from Washington University in 1986 on studies of rhythmic motor pattern generation in the spinal cord. She carried out postdoctoral work cloning ion channel genes in Drosophila with Barry Ganetzky at the University of Wisconsin-Madison, and started her own lab at the University of Wisconsin School of Medicine and Public Health in 1992. She is perhaps best known for work from her lab showing that cardiac IKr is produced by channels encoded by the hERG gene, and for first identifying hERG as the molecular target for acquired long QT syndrome. She was co-inventor of the hERG cell-based safety assay that helps reduce sudden cardiac death due to off-target effects of drugs indicated for a wide range of conditions. Robertson previously received the NSF CAREER Award and was an American Heart Association Established Investigator. She has served on numerous editorial boards and NIH review panels, and was Chair of the 2017 Gordon Research Conference on Cardiac Arrhythmia Mechanisms. Most recently, she received the 2019 Kenneth S. Cole Award in Membrane Biophysics from the Biophysical Society. She is currently Professor in the Department of Neuroscience at the University of Wisconsin School of Medicine and Public Health.

Title of the talk: How to build an action potential: mRNA complexes encode multiple ion channel types during biogenesis

The field has made great strides understanding how ion channels open and close, and how they select for one tiny ion, like potassium, over another, like sodium. A new frontier of ion channel biology is the question of how ion channels, which are often made up of multiple subunits, are formed. In one study we found that the mRNA transcripts encoding the two subunits that make up cardiac IKr channels are themselves associated in a way that ensures the nascent proteins, while they emerge from the protein-synthesizing machinery, interact with each other.

A bigger question is how the balance of ion channels is achieved to ensure an action potential of the right duration in the heart, or frequency of firing in the brain. There must be mechanisms at multiple levels contributing to this precise control, perturbation of which can lead to diseases such as catastrophic cardiac arrhythmias or epilepsy. We are currently examining mechanisms by which the numbers of different ion channel types, or the “stoichiometry of excitability,” is regulated during channel biogenesis as the proteins are synthesized. For these studies we are using innovative molecular biology approaches, single-molecule fluorescence of mRNA and protein, and patch clamp electrophysiology. My lecture will present the latest advances in this work.

Monday, September 30, at 15:00 in Air and Fire

Stirling Churchman

Harvard Medical School and MIT, USA

Stirling Churchman serves as Associate Professor of Genetics at Harvard Medical School and as an Associate Member of the Broad Institute. She obtained a PhD in Physics at Stanford University (2008) and performed her postdoctoral training at UCSF. Since 2011 she leads a group at Harvard Medical School focus on the quantitatively visualization of gene expression processes at higher levels of resolution.

Title of the talk: Orchestrating the many regulatory layers of gene expression

The Churchman lab addresses questions regarding gene regulatory processes occurring throughout the cell, from the nucleus to the mitochondria. We develop tools for tackling critical problems in gene regulation, focusing on three areas. First, we are investigating how regulation of nascent transcription controls RNA levels, alternative splicing, enhancer function and production of non-coding RNAs. We established native elongating transcript sequencing (NET-seq) that measures RNA polymerase density genome-wide at single-nucleotide resolution and has shed new light on how transcription is regulated. Second, we are exploring the connection between splicing and transcription by developing tools that determine when, where, and how splicing occurs co-transcriptionally through careful analysis of nascent RNA sequences. We have developed a NET-seq variant called co-transcriptional processing by nanopore sequencing (nano-COP) that analyzes splicing dynamics in living cells. Finally, we are investigating a fundamental question in eukaryotic gene expression: how are nuclear- and mitochondrial-encoded genes co-regulated? We are capitalizing on our expertise in the development of nuclear genome-wide approaches to comprehensively and accurately probe the mitochondrial genome, enabling significant progress in our understanding of mitochondrial gene expression. This talk will cover our latest progress in these areas.

As part of The Human Protein Atlas program, three new atlases are being released.

The novel databases cover all proteins in blood, brain and metabolism, respectively, and will be made public during a release event on September 5. The r will feature presentations of data findings from the new atlases, opportunities to ask questions, and a celebration mingle. To register your participation, please fill in the form below.

Venue: Gamma 2, SciLifeLab Campus Solna

Host: Mathias Uhlén, Professor KTH Royal Institute of Technology and The Human Protein Atlas program Director

The Human Protein Atlas is a program based at SciLifeLab that started in 2003 with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody – based imaging, mass spectrometry – based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. The current version consists of three separate parts, each focusing on a particular aspect of analysis of the human proteins; including the Tissue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Cell Atlas showing the subcellular localization of proteins in single cells, and the Pathology Atlas showing the impact of protein levels for survival of patients with cancer. The new version (version 19) adds three new parts to the resource, a Blood Atlas showing the profiles of blood cells and proteins in the blood, a Brain Atlas showing the distribution of proteins in human, mouse and pig brain and the Metabolic Atlas showing the presence of metabolic pathways across human tissues. The latter is a collaboration with Chalmers University. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it has been selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation.

Course fee

1300 SEK (includes course dinner, lunches, coffee and snacks)

*Please note that NBIS cannot invoice individuals

Course description

One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof.

Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

Course content

In this course you will learn how to make your data analyses reproducible.
In particular, you will learn:

good practices for data analysis

how to use the version control system git to track edits and collaborate on coding

how to use the package and environment manager Conda

how to use the workflow manager Snakemake

how to use R Markdown to generate automated reports

how to use Jupyter notebooks to document your ongoing analysis

how to use Docker and Singularity to distribute containerized computational environments

Entry requirements

Required for being able to follow the course and to complete computer exercises:

Familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.

Bring your own laptop running Linux or Mac OS (if you run Windows and are interested in participating, please contact the course leaders by email, see above, before applying

Some knowledge in R and/or python is beneficial but not strictly required

Selection criteria

The course can accommodate 20 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from industry.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Would you like to hear the latest on how protein biomarkers are making an impact in areas from wellness profiling to large scale epidemiological initiatives and the identification of a protein signature for ovarian cancer?

“Protein biomarker discovery and implementation – from broad screening to validated signatures and custom panel development“ is being jointly arranged by the Clinical Biomarker facility at SciLifeLab Uppsala and Olink Proteomics. The event will feature presentations from three leading Swedish researchers, after which a lunch will be provided. Attendance is free, but registration is required using the link provided at the end of this email.

Monday September 30 at 15:15

Adam Abate

UCSF, San Francisco, USA

Adam Abate is an Associate Professor at the University of California, San Francisco in the Department of Bioengineering and Therapeutic Sciences (BTS) in the Schools of Medicine and Pharmacy. He is in QB3 and part of the UC Berkeley-UCSF Graduate Program in Bioengineering, PSPG, and iPQB. His research interests are in high-throughput biology with microfluidics, protein engineering through directed evolution, and biophysics.

Title of the talk: Quantitative biology with droplet microfluidics

Many questions at the forefront of biology depend on the interactions of millions of single cells. My lab develops technologies for studying large numbers of single cells. In this talk, I will describe our approaches for sorting cells based on genomic and transcriptomic markers, and performing multi-omics analysis of single cells that allow simultaneous characterization of genomic, transcriptomic, and proteomic signatures. I will also describe how we are adapting these techniques to integrate genomics with other single cell measurement approaches, including imaging, mass spectrometry, and atomic force microscopy. Finally, I will describe how we are using these techniques to build cells into controlled consortia for microbiological studies and bottom-up tissue synthesis.

Monday September 23 at 15:15, Uppsala
Tuesday September 24 at 15:00, Stockholm

The seminar will be held in Uppsala on Monday 23 September 2019, at 15:15 at BMC Uppsala
in Stockholm on Tuesday 24 September 2019, at 15:00 in Gamma 2- lunchroom, SciLifeLab Campus Solna

Prof Geeta Narlikar

Dr. Geeta Narlikar is a Professor in the Department of Biochemistry and Biophysics at the University of California, San Francisco. Her group seeks to uncover the mechanisms by which our genome is folded and compartmentalized to regulate cellular functions.

Title of the talk: Beyond the genetic code: how a shape-shifting genome controls cell identity

Different cell types in a given animal, such as heart cells and brain cells display different behaviors because they express different sets of genes. Yet, they all have DNA with essentially the same sequence and thus the same set of genes. How is it that the same DNA is used to generate different cell types? Which genes are on and which genes are off is controlled in part by how their underlying DNA sequences are packaged. DNA is packaged by wrapping it around specific proteins called histones to generate bead-like structures called nucleosomes. Strings of nucleosomes are then further folded to condense the underlying DNA and make it less accessible. Structures called heterochromatin are thought to be particularly effective at compacting strings of nucleosomes and turning off the underlying genes. A few years ago we discovered that nucleosomes, rather than acting as rigid packaging units act as shape-shifters to regulate access to the wrapped DNA. Around the same time we also found that proteins named HP1 proteins, which are core components of heterochromatin, can sequester packaged DNA into phase-separated droplets. Within these droplets the HP1 molecules are dynamic and display liquid-like properties. In my talk I will discuss the experiments that led to these findings. I will also discuss how these unexpected biophysical properties of the packaged genome are leading to new ways of conceptualizing genome regulation.